Related papers: Estimation of microscopic averages from metadynami…
Recent developments in statistical mechanics have allowed the estimation of equilibrium free energies from the statistics of work measurements during processes that drive the system out of equilibrium. Here a different class of processes is…
The usual formulation of thermodynamics is based on the additivity of macroscopic systems. However, there are numerous examples of macroscopic systems that are not additive, due to the long-range character of the interaction among the…
We propose a method, Temperature Integration, which allows an efficient calculation of free energy differences between two systems of interest, with the same degrees of freedom, which may have rough energy landscapes. The method is based on…
We consider a nearly-elastic model system with one degree of freedom. In each collision with the "wall", the system can either lose or gain a small amount of energy due to stochastic perturbation. The weak limit of the corresponding slow…
Thermodynamic quantities, such as heat and work, are not functions of state, but rather of the process undergone by a physical system. Assessing them can therefore be difficult, since it requires probing the system at least twice. This is…
At low temperatures the configurational phase space of a macroscopic complex system (e.g., a spin-glass) of $N\sim 10^{23}$ interacting particles may split into an exponential number $\Omega_s \sim \exp({\rm const} \times N)$ of ergodic…
We introduce an algorithmic model of heat conduction, the thermodynamic graph. The thermodynamic graph is analogous to meshes in the finite difference method in the sense that the calculation of temperature is carried out at the vertices of…
Out of thermal equilibrium, an environment imposes effective mechanical forces on microscopical nanofabricated devices, chemical or biological systems. Here we address the question of how to calculate these forces together with the response…
Experience collected in mesoscopic dynamic modeling of externally driven systems indicates absence of potentials that could play role of equilibrium or nonequilibrium thermodynamic potentials yet their thermo-dynamics-like modeling is often…
We study thermodynamic processes in contact with a heat bath that may have an arbitrary time-varying periodic temperature profile. Within the framework of stochastic thermodynamics, and for models of thermo-dynamic engines in the idealized…
In the realm of statistical mechanics, it has been established that there is no distinction between the micro-canonical and canonical ensembles in the thermodynamic limit. However, this paradigm may alter when addressing statistical…
The nonequilibrium thermodynamics of an open (classical or quantum) system in strong contact with a single heat bath can be conveniently described in terms of the Hamiltonian of mean force. However, the conventional formulation is limited…
The notion of mean temperature is crucial for a number of fields including climate science, fluid dynamics and biophysics. However, so far its correct thermodynamic foundation is lacking or even believed to be impossible. A physically…
To describe the nonequilibrium states of the system, a new thermodynamic parameter - system lifetime - is introduced. Statistical distributions that describe the behavior of energy and lifetime are recorded. Entropy and obtained…
For classical discrete systems under constant composition typically refferred to substitutional alloys, we propose calculation method of Helmholtz free energy based on a set of special microscopic states. The advantage of the method is that…
The static free energy of glassy systems can be expressed in terms of the Parisi order parameter function. When this function has a discontinuity, the location of the step is determined by maximizing the free energy. In dynamics a…
Understanding kinetics and thermodynamics profile of biomolecules is necessary to understand their functional roles which has a major impact in mechanism driven drug discovery. Molecular dynamics simulation has been routinely used to…
Expectation value of dynamical variables in thermodynamically equilibrium state can be typically provided through well-known canonical average. The average includes tremendous number of possible states considered far beyond practically…
The problem of defining the average kinetic energy of statistical systems is addressed. The conditions of applicability for the formula, relating the average kinetic energy with the mass derivative of the internal energy, are analysed. It…
The average kinetic energy is widely used to characterize temperature in molecular dynamics (MD) simulation. In this letter, the applicability of three types of average kinetic energy as measures of temperature is investigated, i.e., the…